Question

Draw the structure of D-H-Y-K amino acids at PH=7. a) At PH 8, the net charge on the peptide will be....? b) At PH 6, the net charge will be...? c)The PI of this peptide is PH, or equal to PH? I drew the structure but I have no idea how to calculate the net charge at any pH

Answer 1

Ans. Given peptide sequence = DHYK

#a.

Calculation of Charge on peptide:

#I. The residues with acidic side chain and C-terminal are written in RED/BOLD. Their corresponding charge is written in columns of “Acidic residues”. Ignore all other charge/values in “black ink”. The sum of charge in “RED ink” is the total –ve charge on the peptide at specified pH.

#II. The residues with basic side chain and N-terminal are written in Blue/BOLD. Their corresponding charge is written in columns of “Basic residues”. Ignore all other charge/values in “black ink”. The sum of charge in “Blue ink” is the total +ve charge on the peptide at specified pH.

#III. The charge on each residue/ group is calculated using Henderson-Hasselbalch equation as shown in respective column.

#IV. Only residues with acidic and basic side chain are shown in excel for calculation.

#V. pI = Sum of all pKa, pKb or pKc as applicable / No. of groups pKs added

            Hence, pI = 7.055; [see, excel]

#VI.   If pH > pKa, COO- form predominate. If pH < pKa, COOH form predominates

The “acidic” side chain is treated as :-COOH“ group.

At, pH = pKa, the NH2 and NH3+ forms of the amine group exist in equilibrium.

If pH < pKa, NH₃⁺ form predominates. If pH > pKa, NH2 form predominates

The “basic” side chain is treated as “–NH2“group.

Result:

Net charge on peptide at pH 7 = 3.996 = 4.0

Net charge on peptide at pH 8 = 0.980 = 1.0

Net charge on peptide at pH 6 = 1.528 = 1.5

pI = 7.055